Hi Chiarina, I need more information to track the problem. What is the total size of your .scans file in your temporary folder? Can you still add new files to this folder manually (e.g. by copying using Windows Explorer)? Can you check if the same problem occurs if you convert the raw files to mzXML first using readw, and then open them in MZmine? Also, what if you generate a very small raw file (e.g. 1 MB in size), can you still open max 200 of these, or is the limit higher?
Cheers, Tomas On Fri, May 6, 2011 at 10:37 PM, Chiarina Darrah <ch...@psb.vib-ugent.be> wrote: > Hi! Further to the below message, I wanted to have a better > understanding of sample number limits; at the moment in my lab we are > unable to get mzmine to open more than about 200 samples at once. > Attempting any more gets the error message: "There is an error in the > RAW file, please check the log file" But the same RAW files can be > imported successfully if mzmine is restarted, so the files are not > corrupted or anything. The log file , after the "..FINEST....Xcalibur > 2.0 interface initialized" just says "...SEVERE...Unable to open > XCalibur RAW file". > > 200 samples was an improvement from about 120 samples (the previous > limit before getting identical error messages) - when I realised that I > just didn't have enough space on my drive for all the .scans files being > generated in the TEMP folder mzmine was using. Having increased this to > many GB more than needed, then I could indeed open more files. But not > as many as I was expecting. Now, at 200 samples, I have plenty of space > left on the drive (18GB), and I increased the JVM to the 1.3GB max for > the 32-bit system I'm using, and it has 900 MB free when not performing > tasks, and even when performing tasks it is not coming close to maxing out. > > So my question is, what further avenues do I have to increase the no. of > samples - what other things are limiting the no. of samples I can open? > I have a total of 280 samples - it's really annoying to do two batches > because then I have to do the very long-winded downstream processes > twice, working with two separate peak lists when I just want to work > with one within mzmine (I have to work within mzmine as far as I can > tell because I am inspecting MSMS spectra). > > A workaround would be to be able to merge two peaklists - but as far as > I can see, I wouldn't be able to work with MSMS data from all the peaks > on the peak lists unless I had all the raw data open in my project - > which, as I explained above, I can't currently do. > > Thanks for your time! > > Chiarina Darrah > > > > > > > Hi Gözde, > > I have never tried analyzing so many samples at once using MZmine. There > may be a lot of places in MZmine where the code is not optimized for > such high-scale analysis. > Also, it depends on the characteristics of your data (high vs low > resolution, centroided vs continuous spectra etc.). > You may need more RAM than 16GB (there are computers with 1TB of RAM or > more). > You may also split the analysis into separate batches. > > Tomas > > > On Mar 3, 2011, at 11:07 PM, Gözde Gürdeniz wrote: > > > We have been processing the UPLC-QTOF samples with MZmine and it has > worked pretty until now J > > > > However now, I have huge number of samples 5000. I tried to increase > the RAM that MZmine is using according to capacity of my computer > (16 GB RAM that I have). I could manage to process only 1500 samples. I > am working on windows and I guess I can increase the amount of virtual > memory for the use of MZmine by Linux. > > > > Do you think I should go for Linux or is there any other way to solve > this problem of 5000 samples or it does not seem realistic? > > > > > > > > M. Sc, PhD-student > > Gözde Gürdeniz, > > Group of Preventive Nutrition, > > Department of Human Nutrition, > > University of Copenhagen, > > Rolighedsvej 30, DK-1958 Frederiksberg > > Copenhagen-Denmark > > > > E-mail: gozg@... > > Cell Phone: (+45) 29176389 > > > ------------------------------------------------------------------------------ > > Free Software Download: Index, Search & Analyze Logs and other IT > data in > > Real-Time with Splunk. Collect, index and harness all the fast moving > IT data > > generated by your applications, servers and devices whether physical, > virtual > > or in the cloud. Deliver compliance at lower cost and gain new business > > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > > Mzmine-devel mailing list > > Mzmine-devel@... > > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology > 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan > TEL: +81-98-966-8684 > > -- > ================================================================== > Chiarina Darrah > > Tel:+32 (0)9 331 38 85 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > ch...@psb.vib-ugent.be http://www.psb.vib-ugent.be > ================================================================== > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > ------------------------------------------------------------------------------ WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
